Manganese in PDB 5fh3: The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp
Enzymatic activity of The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp
All present enzymatic activity of The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp:
4.1.1.32;
Protein crystallography data
The structure of The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp, PDB code: 5fh3
was solved by
T.A.Johnson,
T.Holyoak,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
59.66 /
1.60
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.699,
119.313,
60.821,
90.00,
107.95,
90.00
|
R / Rfree (%)
|
20.5 /
24.3
|
Other elements in 5fh3:
The structure of The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp
(pdb code 5fh3). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the
The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp, PDB code: 5fh3:
Jump to Manganese binding site number:
1;
2;
3;
Manganese binding site 1 out
of 3 in 5fh3
Go back to
Manganese Binding Sites List in 5fh3
Manganese binding site 1 out
of 3 in the The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn701
b:18.2
occ:1.00
|
OD1
|
A:ASP311
|
1.6
|
7.6
|
0.3
|
O4
|
A:OXL703
|
1.9
|
22.3
|
1.0
|
O1G
|
A:GTP704
|
2.1
|
17.3
|
0.7
|
O3
|
A:OXL703
|
2.2
|
18.9
|
1.0
|
NE2
|
A:HIS264
|
2.3
|
13.6
|
1.0
|
OD1
|
A:ASP311
|
2.4
|
18.5
|
0.7
|
NZ
|
A:LYS244
|
2.5
|
19.1
|
1.0
|
O1G
|
A:GTP704
|
2.6
|
8.9
|
0.3
|
CG
|
A:ASP311
|
2.7
|
9.1
|
0.3
|
C2
|
A:OXL703
|
2.7
|
24.1
|
1.0
|
C1
|
A:OXL703
|
2.8
|
23.7
|
1.0
|
OD2
|
A:ASP311
|
3.2
|
8.8
|
0.3
|
PG
|
A:GTP704
|
3.2
|
18.5
|
0.7
|
CD2
|
A:HIS264
|
3.2
|
14.2
|
1.0
|
CE1
|
A:HIS264
|
3.3
|
13.9
|
1.0
|
CG
|
A:ASP311
|
3.4
|
17.9
|
0.7
|
O2G
|
A:GTP704
|
3.6
|
17.7
|
0.7
|
CE
|
A:LYS244
|
3.6
|
21.2
|
1.0
|
OD2
|
A:ASP311
|
3.6
|
18.0
|
0.7
|
PG
|
A:GTP704
|
3.7
|
8.7
|
0.3
|
O2
|
A:OXL703
|
3.9
|
26.9
|
1.0
|
NZ
|
A:LYS290
|
3.9
|
16.9
|
0.7
|
O3G
|
A:GTP704
|
4.0
|
19.5
|
0.7
|
CB
|
A:ASP311
|
4.0
|
9.4
|
0.3
|
O1
|
A:OXL703
|
4.1
|
25.0
|
1.0
|
O3G
|
A:GTP704
|
4.1
|
9.1
|
0.3
|
CE
|
A:LYS290
|
4.2
|
8.1
|
0.3
|
O
|
A:HOH805
|
4.2
|
19.5
|
1.0
|
O
|
A:HOH908
|
4.2
|
19.7
|
1.0
|
NZ
|
A:LYS290
|
4.2
|
8.0
|
0.3
|
O2G
|
A:GTP704
|
4.3
|
9.1
|
0.3
|
CE
|
A:LYS290
|
4.3
|
16.5
|
0.7
|
ND1
|
A:HIS264
|
4.4
|
13.8
|
1.0
|
CG
|
A:HIS264
|
4.4
|
13.6
|
1.0
|
O3B
|
A:GTP704
|
4.5
|
18.9
|
0.7
|
CA
|
A:ASP311
|
4.6
|
9.9
|
0.3
|
CB
|
A:ASP311
|
4.8
|
18.1
|
0.7
|
O
|
A:ASP311
|
4.8
|
11.3
|
0.3
|
CB
|
A:SER286
|
4.9
|
23.1
|
0.7
|
O
|
A:HOH1056
|
4.9
|
39.8
|
1.0
|
CD
|
A:LYS244
|
5.0
|
20.2
|
1.0
|
CZ
|
A:PHE485
|
5.0
|
19.1
|
1.0
|
|
Manganese binding site 2 out
of 3 in 5fh3
Go back to
Manganese Binding Sites List in 5fh3
Manganese binding site 2 out
of 3 in the The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn702
b:17.9
occ:0.70
|
MN
|
A:MN702
|
0.0
|
17.9
|
0.7
|
MN
|
A:MN702
|
1.3
|
6.3
|
0.3
|
OG1
|
A:THR291
|
1.7
|
8.9
|
0.3
|
O
|
A:HOH817
|
1.9
|
22.3
|
1.0
|
O
|
A:HOH805
|
2.0
|
19.5
|
1.0
|
OG1
|
A:THR291
|
2.1
|
16.3
|
0.7
|
O3G
|
A:GTP704
|
2.2
|
19.5
|
0.7
|
O1B
|
A:GTP704
|
2.2
|
17.7
|
0.7
|
OD2
|
A:ASP310
|
2.5
|
8.3
|
0.3
|
O
|
A:HOH815
|
2.5
|
25.8
|
1.0
|
O1B
|
A:GTP704
|
3.0
|
9.1
|
0.3
|
CB
|
A:THR291
|
3.2
|
8.8
|
0.3
|
CG
|
A:ASP310
|
3.2
|
8.2
|
0.3
|
O3G
|
A:GTP704
|
3.3
|
9.1
|
0.3
|
CB
|
A:THR291
|
3.3
|
16.6
|
0.7
|
PG
|
A:GTP704
|
3.3
|
18.5
|
0.7
|
PB
|
A:GTP704
|
3.4
|
18.6
|
0.7
|
O
|
A:ASP310
|
3.5
|
8.5
|
0.3
|
OD2
|
A:ASP310
|
3.6
|
17.2
|
0.7
|
O3B
|
A:GTP704
|
3.6
|
18.9
|
0.7
|
OD1
|
A:ASP310
|
3.8
|
8.1
|
0.3
|
CB
|
A:ASP310
|
3.9
|
8.2
|
0.3
|
CA
|
A:THR291
|
3.9
|
8.7
|
0.3
|
O1G
|
A:GTP704
|
3.9
|
17.3
|
0.7
|
CG2
|
A:THR291
|
4.0
|
8.8
|
0.3
|
N
|
A:THR291
|
4.0
|
8.5
|
0.3
|
O
|
A:HOH908
|
4.0
|
19.7
|
1.0
|
O1A
|
A:GTP704
|
4.0
|
22.4
|
0.7
|
N
|
A:THR291
|
4.1
|
16.8
|
0.7
|
C
|
A:ASP310
|
4.2
|
8.7
|
0.3
|
CA
|
A:THR291
|
4.2
|
16.2
|
0.7
|
O
|
A:ASP310
|
4.3
|
16.2
|
0.7
|
NH1
|
A:ARG405
|
4.3
|
21.2
|
0.7
|
PB
|
A:GTP704
|
4.3
|
8.9
|
0.3
|
PG
|
A:GTP704
|
4.4
|
8.7
|
0.3
|
CG2
|
A:THR291
|
4.4
|
16.5
|
0.7
|
CG
|
A:ASP310
|
4.4
|
17.1
|
0.7
|
O2B
|
A:GTP704
|
4.4
|
18.8
|
0.7
|
OD1
|
A:ASP311
|
4.5
|
18.5
|
0.7
|
O3A
|
A:GTP704
|
4.5
|
19.3
|
0.7
|
CA
|
A:GLY334
|
4.5
|
17.3
|
0.7
|
O
|
A:HOH966
|
4.6
|
27.5
|
1.0
|
O2G
|
A:GTP704
|
4.6
|
17.7
|
0.7
|
CA
|
A:GLY334
|
4.6
|
7.0
|
0.3
|
O1G
|
A:GTP704
|
4.6
|
8.9
|
0.3
|
N
|
A:VAL335
|
4.7
|
16.4
|
0.7
|
CB
|
A:ASP311
|
4.7
|
9.4
|
0.3
|
CA
|
A:ASP310
|
4.7
|
8.2
|
0.3
|
O
|
A:HOH818
|
4.7
|
27.7
|
1.0
|
O3B
|
A:GTP704
|
4.7
|
8.9
|
0.3
|
PA
|
A:GTP704
|
4.8
|
22.9
|
0.7
|
O
|
A:PHE333
|
4.9
|
17.2
|
0.7
|
OD1
|
A:ASP311
|
4.9
|
7.6
|
0.3
|
CB
|
A:LYS290
|
4.9
|
8.3
|
0.3
|
CB
|
A:LYS290
|
4.9
|
16.6
|
0.7
|
C
|
A:LYS290
|
4.9
|
8.4
|
0.3
|
O
|
A:PHE333
|
5.0
|
6.9
|
0.3
|
N
|
A:ASP311
|
5.0
|
9.4
|
0.3
|
|
Manganese binding site 3 out
of 3 in 5fh3
Go back to
Manganese Binding Sites List in 5fh3
Manganese binding site 3 out
of 3 in the The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn702
b:6.3
occ:0.30
|
MN
|
A:MN702
|
0.0
|
6.3
|
0.3
|
MN
|
A:MN702
|
1.3
|
17.9
|
0.7
|
O3G
|
A:GTP704
|
1.5
|
19.5
|
0.7
|
O1B
|
A:GTP704
|
1.8
|
17.7
|
0.7
|
O
|
A:HOH815
|
1.9
|
25.8
|
1.0
|
O1B
|
A:GTP704
|
2.1
|
9.1
|
0.3
|
O3G
|
A:GTP704
|
2.2
|
9.1
|
0.3
|
OG1
|
A:THR291
|
2.2
|
8.9
|
0.3
|
PG
|
A:GTP704
|
2.5
|
18.5
|
0.7
|
O3B
|
A:GTP704
|
2.6
|
18.9
|
0.7
|
PB
|
A:GTP704
|
2.6
|
18.6
|
0.7
|
O
|
A:HOH817
|
2.6
|
22.3
|
1.0
|
O
|
A:HOH805
|
2.7
|
19.5
|
1.0
|
OG1
|
A:THR291
|
3.2
|
16.3
|
0.7
|
O1A
|
A:GTP704
|
3.2
|
22.4
|
0.7
|
PG
|
A:GTP704
|
3.3
|
8.7
|
0.3
|
PB
|
A:GTP704
|
3.3
|
8.9
|
0.3
|
CB
|
A:THR291
|
3.4
|
8.8
|
0.3
|
O1G
|
A:GTP704
|
3.5
|
17.3
|
0.7
|
O3A
|
A:GTP704
|
3.5
|
19.3
|
0.7
|
O3B
|
A:GTP704
|
3.6
|
8.9
|
0.3
|
O2G
|
A:GTP704
|
3.6
|
17.7
|
0.7
|
OD2
|
A:ASP310
|
3.7
|
8.3
|
0.3
|
PA
|
A:GTP704
|
3.8
|
22.9
|
0.7
|
NH1
|
A:ARG405
|
3.8
|
21.2
|
0.7
|
O1G
|
A:GTP704
|
3.9
|
8.9
|
0.3
|
O2B
|
A:GTP704
|
4.0
|
18.8
|
0.7
|
O1A
|
A:GTP704
|
4.0
|
9.1
|
0.3
|
CB
|
A:THR291
|
4.1
|
16.6
|
0.7
|
N
|
A:THR291
|
4.1
|
8.5
|
0.3
|
CG2
|
A:VAL335
|
4.1
|
18.4
|
0.7
|
N
|
A:VAL335
|
4.2
|
16.4
|
0.7
|
CA
|
A:THR291
|
4.3
|
8.7
|
0.3
|
NH1
|
A:ARG405
|
4.3
|
8.4
|
0.3
|
O
|
A:HOH908
|
4.4
|
19.7
|
1.0
|
O2B
|
A:GTP704
|
4.4
|
8.8
|
0.3
|
O2A
|
A:GTP704
|
4.4
|
20.3
|
0.7
|
O3A
|
A:GTP704
|
4.4
|
9.0
|
0.3
|
CG2
|
A:THR291
|
4.4
|
8.8
|
0.3
|
CA
|
A:GLY334
|
4.4
|
7.0
|
0.3
|
O
|
A:ASP310
|
4.4
|
8.5
|
0.3
|
CG
|
A:ASP310
|
4.5
|
8.2
|
0.3
|
O
|
A:HOH818
|
4.5
|
27.7
|
1.0
|
N
|
A:THR291
|
4.6
|
16.8
|
0.7
|
O2G
|
A:GTP704
|
4.6
|
9.1
|
0.3
|
CB
|
A:VAL335
|
4.7
|
18.2
|
0.7
|
N
|
A:VAL335
|
4.7
|
7.3
|
0.3
|
CA
|
A:GLY334
|
4.7
|
17.3
|
0.7
|
PA
|
A:GTP704
|
4.8
|
9.2
|
0.3
|
CZ
|
A:ARG405
|
4.8
|
21.4
|
0.7
|
O
|
A:PHE333
|
4.9
|
6.9
|
0.3
|
OD2
|
A:ASP310
|
4.9
|
17.2
|
0.7
|
OD1
|
A:ASP311
|
4.9
|
18.5
|
0.7
|
CB
|
A:LYS290
|
4.9
|
8.3
|
0.3
|
CA
|
A:THR291
|
5.0
|
16.2
|
0.7
|
NH2
|
A:ARG405
|
5.0
|
20.9
|
0.7
|
O3
|
A:OXL703
|
5.0
|
18.9
|
1.0
|
|
Reference:
T.A.Johnson,
M.J.Mcleod,
T.Holyoak.
Utilization of Substrate Intrinsic Binding Energy For Conformational Change and Catalytic Function in Phosphoenolpyruvate Carboxykinase. Biochemistry V. 55 575 2016.
ISSN: ISSN 0006-2960
PubMed: 26709450
DOI: 10.1021/ACS.BIOCHEM.5B01215
Page generated: Sun Oct 6 00:13:10 2024
|